Saline acid-sulfate soils limit crop production due to acidity, salinity, toxicity, and nutrient deficiencies. Although biochar, lime, and cow manure are individually known to enhance soil physiochemical quality, their combined effects on these constraints and vegetable growth remain insufficiently understood. This study evaluates the combined effects of biochar, lime, and cow manure on saline acid-sulfate soil constraints and identifies key factors affecting Pak Choy (Brassica rapa L.) growth. A field randomized complete block design with four replicates was conducted over two seasons with six treatments: control (no amendment), lime, cow manure, biochar, biochar-lime, and biochar-cow manure, applied at standard rates. The five amendment treatments improved soil constraints like acidity, toxicity, and nutrient deficiencies by 32–128%, while decreasing salinity by 25–26% compared to the control. The biochar–cow manure combination most effectively improved soil nutrient status, increasing Pak Choy biomass by more than 200% compared with the sole amendments and the biochar–lime treatment. In contrast, the biochar–lime combination was most effective in alleviating soil acidity and metal toxicity, resulting in a higher soil quality index (0.67–0.69), relative to the control (0.33–0.35). Overall, biochar and cow manure synergistically enhanced nutrient availability and vegetable growth, whereas biochar and lime were more effective in correcting acidity and toxicity but produced comparatively smaller yield gains due to limited nutrient enhancement. These results underscore the potential of tailored amendments, especially biochar and cow manure, to enhance vegetable production in saline acid-sulfate soils, supporting sustainable agriculture in challenging environments.